I suspect she is just a victim of all of the myths. It is "common knowledge" that intact penises are inherently dirty and are prone to infections and are hard to clean. She was just reacting to these myths. If she has a daughter, she probably has had to deal with hygiene issues that are hard and do need attention and was transferring those experiences to your son.
I'm sure she had no malicious intent but was trying to do the best she could with the misconceptions she harbors. Instead of being angry with her, explain the function of the foreskin in protecting the glans and meatus and how it is counter productive to try to clean more than the outside. To us, it makes complete sense but to someone who has been subjected to the myths all of their adult life and is not educated to mother nature's perfect design, they will do what is completely wrong while they are diligently trying to do their best.